Technical Genomics FAQ Hub

Q: What is the difference between 16S rRNA and Shotgun Metagenomics?

16S rRNA sequencing targets specific hypervariable regions to identify bacterial taxa. Shotgun metagenomics sequences all genomic DNA in a sample, providing functional pathway profiling and species/strain-level resolution across all domains of life (bacteria, viruses, fungi).

Advanced answers for researchers, clinicians, and biotech professionals working with complex genomic data.

Sanger Sequencing Services

What is the typical read length and accuracy for Sanger Sequencing?

Our standard Sanger Sequencing provides a Phred Quality Score of Q20 or higher (99% accuracy), with typical contiguous read lengths ranging from 800 to 1,000 base pairs (bp), depending on the template quality and primer specificity.

How do you handle GC-rich or secondary structure templates?

We utilize specialized sequencing chemistries, including the addition of DMSO, betaine, and high-temperature denaturing protocols (up to 98°C) to successfully resolve complex hairpins and GC-rich regions (>70%) that typically cause polymerase slippage.

What is the maximum template size you can sequence via primer walking?

Using a strategic primer walking approach with 100-150 bp overlaps, we can sequence constructs, plasmids, and BACs up to 10kb in length on both strands to ensure consensus accuracy.

How should I design primers for Sanger sequencing?

Primers should ideally be 18-24 nucleotides long, with a GC content of 40-60%, and a melting temperature (Tm) between 55°C and 60°C. Please ensure your primer binding site is at least 40-50 bp away from your region of interest to account for the initial loss of resolution in the chromatogram.

Next Generation Sequencing (NGS)

What is the recommended sequencing depth for WES vs. WGS?

For clinical applications, we recommend a minimum coverage depth of 100x for Whole Exome Sequencing (WES) to ensure accurate variant calling in coding regions. For Whole Genome Sequencing (WGS), a depth of 30x is the industry gold standard for detecting structural variants and single nucleotide polymorphisms (SNPs).

What is the difference between 16S rRNA and Shotgun Metagenomics?

16S rRNA sequencing targets specific hypervariable regions (like V3-V4) to identify and quantify bacterial taxa. Shotgun metagenomics indiscriminately sequences all genomic DNA in a sample, providing not just taxonomic classification down to the strain level, but also functional pathway profiling across bacteria, viruses, and fungi.

How do you handle rRNA depletion in RNA-Seq workflows?

For whole transcriptome analysis, we utilize magnetic bead-based ribodepletion kits (such as Ribo-Zero Plus) to efficiently remove cytoplasmic, mitochondrial, and chloroplast ribosomal RNA prior to library preparation. This maximizes sequencing real estate for informative mRNA and lncRNA transcripts.

What bioinformatics deliverables are included with NGS projects?

Standard deliverables include raw data (FASTQ), alignment files (BAM/CRAM), and variant call files (VCF). We provide customized pipelines including Differential Gene Expression (DGE), Gene Ontology (GO) enrichment, and comprehensive HTML reports with PCA plots and heatmaps.

Medical & Clinical Genomics

Do you offer targeted gene panels for oncology profiling?

Yes, we provide both pan-cancer and specific somatic mutation panels (e.g., BRCA1/2, EGFR, KRAS) with ultra-high sequencing depth (>500x to >1000x). This allows for the confident detection of low-frequency variants and subclonal mutations in heterogeneous tumor tissue, including FFPE samples.

Are your clinical variant interpretations based on ACMG guidelines?

Yes. All clinical variant curation and interpretations are strictly performed in accordance with the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) framework.

How do you report incidental or secondary findings?

We follow the latest ACMG recommendations for reporting secondary findings in highly penetrant, medically actionable genes (e.g., familial hypercholesterolemia, Lynch syndrome), provided the patient has not explicitly opted out during the pre-test informed consent process.

Personal Genomics

What is the difference between microarray genotyping and WGS for personal genomics?

Microarray genotyping relies on specific probes to identify hundreds of thousands of known genetic variants (SNPs). Whole Genome Sequencing (WGS) reads your entire 3 billion base pair genome, allowing for the discovery of both known variants and completely novel rare mutations unique to your lineage.

Do you provide raw data access to consumers?

Yes, we believe your genomic data belongs to you. Upon completion of sequencing, clients can securely download their raw FASTQ files and annotated VCF files for use with third-party bioinformatics analysis tools or genetic counselors.

How is my genetic data secured and anonymized?

Data security is paramount. All genomic data is immediately de-identified upon sample accessioning using alphanumeric barcodes. Data is stored on AES-256 encrypted, access-controlled servers and is never sold or shared with pharmaceutical or third-party entities.

Sample Logistics & Transport

How do I ship FFPE (Formalin-Fixed Paraffin-Embedded) blocks or slides?

FFPE blocks and unstained slides should be shipped at ambient temperature. Ensure slides are securely packed in specialized slide mailers to prevent mechanical breakage during transit, and protect wax blocks from prolonged exposure to extreme heat.

What are the cold-chain requirements for shipping RNA samples?

Extracted RNA is highly susceptible to RNase degradation. Purified RNA samples must be shipped on dry ice to maintain a strict temperature of -80°C. Alternatively, tissues can be shipped submerged in RNAlater® stabilization solution at room temperature.

What is your policy on long-term sample retention?

Extracted nucleic acids (DNA/RNA) are routinely stored in our -80°C biorepository for 90 days post-reporting. If you require extended biobanking services for longitudinal studies, this can be arranged under a separate service level agreement.

Ready to optimize your genomic research?

Our senior bioinformatics team is available to assist with experimental design, library prep optimization, and custom pipeline development.

Consult With Our Experts

Yaazh Xenomics,
Module No. 103,
TICEL BIOPARK Phase – III,
1st floor, Maruthamalai Road,
Coimbatore - 641046.
Tamil Nadu, India

Yaazh Xenomics,
No.9-6, Sritej Nagar,
Anandapuram,
Visakhapatnam -531022.
Andhra Pradesh

Yaazh Xenomics,
Ground Floor, Plot No.17-R1,
120 feet Road,
Vivekananda Nagar,
Sambakulam, Madurai - 625 007,
Tamil Nadu. Indi

+91 9943132020 +91 9500245454info@yaazhxenomics.com

Yaazh Xenomics is a leading biotechnology company based in Coimbatore, Tamil Nadu, India, specializing in comprehensive genomic solutions. As a DNA testing laboratory, we offer a broad spectrum of services, including DNA sequencing, RNA Sequencing, Sanger Sequencing, 16s rRNA, 18s rRNA, ITS, COI, RBCL, Matk gene Sequencing for DNA Barcoding, gene expression analysis, SNP analysis, Next-Generation Sequencing (NGS), Various Medical Genome testing, Exome Sequencing, Gut Microbiome Test, Metagenome Sequencing, Whole Genome Sequencing (WGS), Transcriptome Sequencing using advance NGS platforms like Nanopore, Illumina, MGI, Thermo. Also, we provide advance Bioinformatics, Customized Bioinformatics and a variety of other genetic testing and Molecular testing.